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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SHROOM4 Gene

protein-coding   GIFtS: 47
GCID: GC0XM050351

shroom family member 4

 Explore 6 diseases affiliated with
SHROOM4 via our new
 Human Malady Compendium 
Biological research products
for SHROOM4
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Shroom Family Member 41 2
KIAA12021 3 5
Second Homolog Of Apical Protein2 3
SHAP2 3
Protein Shroom42
SDSX5

External Ids:    HGNC: 292151   Entrez Gene: 574772   Ensembl: ENSG000001583527   OMIM: 3005795   UniProtKB: Q9ULL83   
ORGUL members:         
NONCODE:n407652    

Export aliases for SHROOM4 gene to outside databases

Previous GC identifer: GC0XM047778


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for SHROOM4:
This gene encodes a member of the APX/Shroom family, which contain an N-terminal PDZ domain and a C-terminal ASD2
motif. The encoded protein may play a role in cytoskeletal architecture. Mutations in this gene have been linked to
Stocco dos Santos X-linked mental retardation syndrome. Alternatively spliced transcript variants have been described.
(provided by RefSeq, Mar 2009)

UniProtKB/Swiss-Prot: SHRM4_HUMAN, Q9ULL8
Function: Probable regulator of cytoskeletal architecture that plays an important role in development. May regulate
cellular and cytoskeletal architecture by modulating the spatial distribution of myosin II (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.1  NT_011638.13  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SHROOM4 gene promoter:
         Nkx3-1   Nkx3-1 v4   Nkx2-2   RelA   Nkx3-1 v1   Nkx2-5   NF-kappaB   Nkx3-1 v2   Nkx3-1 v3   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSHROOM4 promoter sequence
   Search SABiosciences Chromatin IP Primers for SHROOM4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SHROOM4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xp11.22   Ensembl cytogenetic band:  Xp11.22   HGNC cytogenetic band: Xp11.22

SHROOM4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SHROOM4 gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM050351:  view genomic region     (about GC identifiers)

Start:
50,334,642 bp from pter      End:
50,557,302 bp from pter
Size:
222,661 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: SHRM4_HUMAN, Q9ULL8 (See protein sequence)
Recommended Name: Protein Shroom4  
Size: 1493 amino acids; 164857 Da
Subunit: Interacts directly with F-actin (By similarity)
Subcellular location: Cytoplasm, cytoskeleton. Note=Shows partial colocalization with the cytoplasmic pool of F-actin
Sequence caution: Sequence=BAA86516.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=CAM13070.1; Type=Erroneous gene model prediction;
1 PDB 3D structure from and Proteopedia for SHROOM4:
2EDP (3D)    
Secondary accessions: A7E2X9 D6RFW0 Q96LA0
Alternative splicing: 2 isoforms:  Q9ULL8-1   Q9ULL8-2   

Explore the universe of human proteins at neXtProt for SHROOM4: NX_Q9ULL8

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9ULL8

  • SHROOM4 Protein expression data from MOPED and PaxDb:    About this image 
    SHROOM4 Protein Expression
    REFSEQ proteins: NP_065768.2  
    ENSEMBL proteins: 
     ENSP00000289292   ENSP00000421450   ENSP00000365188  

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    Uscn Proteins for SHROOM4

    Gene Ontology (GO): 5/11 cellular component terms (GO ID links to tree view) (see all 11):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001725colocalizes with stress fiber ISS--
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm ISS--
    GO:0009898internal side of plasma membrane IDA16249884

    SHROOM4 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    SHROOM4 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR001478 PDZ
     IPR014799 ASD2

    Graphical View of Domain Structure for InterPro Entry Q9ULL8

    ProtoNet protein and cluster: Q9ULL8

    UniProtKB/Swiss-Prot: SHRM4_HUMAN, Q9ULL8
    Similarity: Belongs to the Shroom family
    Similarity: Contains 1 ASD2 domain
    Similarity: Contains 1 PDZ (DHR) domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, Sirion Biotech, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, Sirion Biotech, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SHRM4_HUMAN, Q9ULL8
    Function: Probable regulator of cytoskeletal architecture that plays an important role in development. May regulate
    cellular and cytoskeletal architecture by modulating the spatial distribution of myosin II (By similarity)

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0051015actin filament binding ISS--
         
    SHROOM4 for ontologies           About GeneDecksing


    Animal Models:
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    In Situ Assay
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SHROOM4

    STRING Interaction Network Preview (showing 5 interactants - click image to see 22)

    5/22 Interacting proteins for SHROOM4 (ENSP000002892924) via UniProtKB, MINT, STRING, and/or I2D (see all 22)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MYBPC3ENSP000003821934STRING: ENSP00000382193
    MYH1ENSP000002262074STRING: ENSP00000226207
    MYH10ENSP000002692434STRING: ENSP00000269243
    MYH11ENSP000003796164STRING: ENSP00000379616
    MYH13ENSP000002521724STRING: ENSP00000252172
    About this table

    Gene Ontology (GO): 5 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000902NOT cell morphogenesis IDA16684770
    GO:0007015actin filament organization ISS--
    GO:0007420brain development IDA16249884
    GO:0030036actin cytoskeleton organization NAS16684770
    GO:0050890cognition IDA16249884

    SHROOM4 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SHROOM4
    Search CenterWatch for drugs/clinical trials and news about SHROOM4 / SHRM4 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SHROOM4 gene: 
    NM_020717.3  

    Unigene Cluster for SHROOM4:

    Shroom family member 4
    Hs.420541  [show with all ESTs]
    Unigene Representative Sequence: NM_020717
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000289292(uc004dpd.3) ENST00000483955 ENST00000460112(uc004dpf.1)
    ENST00000484922 ENST00000376020(uc004dpe.2)

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    hsa-miR-4291 hsa-miR-100* hsa-miR-642a hsa-miR-1197 hsa-miR-15a hsa-miR-218-1* hsa-miR-29a hsa-miR-765
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    Additional cDNA sequence: 

    AB033028.1 AK092659.1 AK127486.1 AY044234.1 BC151240.1 NR_027121.1 

    4 DOTS entries:

    DT.102766  DT.95285309  DT.100013026  DT.430767 

    24/34 AceView cDNA sequences (see all 34):

    AW473467 H67589 AL707209 AY044234 AW001038 CK902532 AK092659 AW972020 
    AI005420 BQ016983 BU682945 AB033028 AA515902 CK902533 BX472125 BU078027 
    BU078275 AV729515 AK127486 BU194023 AI381269 BF325729 BE890569 BF107195 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SHROOM4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --
    SHROOM4 Expression
    About this image

    SHROOM4 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table

    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Definitive endoderm-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See SHROOM4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SHROOM4

    SOURCE GeneReport for Unigene cluster: Hs.420541

    UniProtKB/Swiss-Prot: SHRM4_HUMAN, Q9ULL8
    Tissue specificity: Expressed in all fetal and adult tissues investigated. Expressed in adult heart, brain, placenta,
    lung, liver, skeletal muscle, kidney and pancreas. In brain regions detected in cerebellum, cerebral cortex, medulla,
    spinal cord, occipital pole, frontal lobe, temporal lobe and putamen. The expression is strongest in the medulla and
    weakest in the cerebral cortex

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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for SHROOM4 gene from 3/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia SHROOM46
    --
    37(a)
    1 ↔ 1
    GL343577.1(12512-48912)
    zebrafish
    (Danio rerio)
    Actinopterygii shroom46
    shroom family member 4
    27(a)
    1 ↔ 1
    7(25896649-25980111)
    fruit fly
    (Drosophila melanogaster)
    Insecta Shroom6
    Shroom
    9(a)
    1 → many
    2R(10195667-10239312)


    ENSEMBL Gene Tree for SHROOM4 (if available)
    TreeFam Gene Tree for SHROOM4 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SHROOM4 gene
    SHROOM12  SHROOM32  SHROOM22  
    1 SIMAP similar gene for SHROOM4 using alignment to 1 protein entry:     SHRM4_HUMAN:
    DKFZp781J074

    SHROOM4 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/2381 NCBI SNPs in SHROOM4 are shown (see all 2381    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1892561231,2
    --50334177(+) ATTTCC/TCTTGG 2 -- ds50010--------
    rs1389893031,2
    --50334284(+) CCACAC/TTGTCT 2 -- ds50010--------
    rs66145461,2
    C,F,A,H--50334425(+) CTTACG/ACAAGG 2 -- ds500118Minor allele frequency- A:0.32NS EA WA NA 1985
    rs23162021,2
    C,H--50334455(-) ATCCAA/GTGCTT 2 -- ds50019Minor allele frequency- G:0.00WA NA CSA 16
    rs1847691361,2
    --50334603(+) AGTTTC/TGCACT 2 -- ds50010--------
    rs761046271,2
    C--50334676(+) TTCTTG/TCTTTC 2 -- nc-transcript-variantut310--------
    rs771714871,2
    C--50334694(+) CTTTCG/TTTTCT 2 -- nc-transcript-variantut310--------
    rs59152761,2
    C,F,A,H--50334780(+) TGGTGC/TGGTCT 2 -- nc-transcript-variantut31 ese36Minor allele frequency- T:0.25NA WA CSA 12
    rs28730981,2
    C,F,A,H--50335008(-) CGGGCG/ATGGTG 2 -- ut31 nc-transcript-variant5Minor allele frequency- A:0.18WA NA 11
    rs1879737161,2
    --50335017(+) CGGCCA/GGAACT 2 -- ut31 nc-transcript-variant0--------

    HapMap Linkage Disequilibrium report for SHROOM4 (50334642 - 50557302 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for SHROOM4
         1 Indel: 47817
    Human Gene Mutation Database (HGMD): SHROOM4

    Locus Specific Mutation Databases (LSDB): SHROOM4

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SHROOM4 for disorders           About GeneDecksing

    OMIM gene information: 300579   
    OMIM disorders: 300434  
    UniProtKB/Swiss-Prot: SHRM4_HUMAN, Q9ULL8
  • Defects in SHROOM4 are the cause of mental retardation syndromic X-linked Stocco dos Santos type (SDSX)
  • [MIM:300434]. A syndrome characterized by severe mental retardation with hyperactivity, aggressive behavior, delayed
    or no speech, and seizures. Additional features include congenital bilateral hip luxation, short stature, and kyphosis
  • Note=A chromosomal aberration involving SHROOM4 is a cause of X-linked mental retardation (XLMR).
  • Translocation t(X;8)(p11.22;p23.3) with FBXO25
  • Note=A chromosomal aberration involving SHROOM4 is a cause of X-linked mental retardation (XLMR).
  • Translocation t(X;19)

    6 diseases for SHROOM4:    About MalaCards
    stocco dos santos x-linked mental retardation syndrome    mental retardation syndrome    hip luxation    short stature
    intellectual disability    cerebritis


    Export disorders for SHROOM4 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SHROOM4 gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with SHROOM4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A new standard nomenclature for proteins related to Apx and Shroom. (PubMed id 16615870)1, 2, 3 Hagens O....Wallingford J.B. (2006)
    2. Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10574462)1, 2, 3 Nagase T.... Ohara O. (1999)
    3. Disruptions of the novel KIAA1202 gene are associated with X-linked mental retardation. (PubMed id 16249884)1, 2 Hagens O.... Hanauer A. (2006)
    4. Differential actin-dependent localization modulates the evolutionarily conserved activity of Shroom family proteins. (PubMed id 16684770)1, 2 Dietz M.L.... Hildebrand J.D. (2006)
    5. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    6. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (2005)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (2004)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
    9. Stocco dos Santos X-linked mental retardation syndrome: clinical elucidation and localization to Xp11.3-Xq21.3. (PubMed id 12673656)1 Stocco dos Santos R.C....Schwartz C.E. (2003)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 57477 HGNC: 29215 AceView: KIAA1202 Ensembl:ENSG00000158352 euGenes: HUgn57477
    ECgene: SHROOM4 H-InvDB: SHROOM4

    (According to HUGE)
    About This Section
    HUGE: KIAA1202

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SHROOM4 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SHROOM4 gene:
    Search GeneIP for patents involving SHROOM4

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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